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- PDB-4g5o: Structure of LGN GL4/Galphai3(Q147L) complex -

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Basic information

Entry
Database: PDB / ID: 4g5o
TitleStructure of LGN GL4/Galphai3(Q147L) complex
Components
  • G-protein-signaling modulator 2
  • Guanine nucleotide-binding protein G(k) subunit alpha
KeywordsCELL CYCLE/SIGNALING PROTEIN / Galphai / GoLoco / Galpha signaling / asymmetric cell division / CELL CYCLE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


Ran protein signal transduction / lateral cell cortex / maintenance of centrosome location / cell cortex region / positive regulation of spindle assembly / G alpha (i) signalling events / negative regulation of adenylate cyclase activity / GTP metabolic process / GDP-dissociation inhibitor activity / dopamine receptor signaling pathway ...Ran protein signal transduction / lateral cell cortex / maintenance of centrosome location / cell cortex region / positive regulation of spindle assembly / G alpha (i) signalling events / negative regulation of adenylate cyclase activity / GTP metabolic process / GDP-dissociation inhibitor activity / dopamine receptor signaling pathway / dynein complex binding / mitotic spindle pole / establishment of mitotic spindle orientation / positive regulation of macroautophagy / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / G-protein alpha-subunit binding / lateral plasma membrane / regulation of mitotic spindle organization / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / mitotic spindle organization / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / ADP signalling through P2Y purinoceptor 12 / G alpha (z) signalling events / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / GDP binding / heterotrimeric G-protein complex / : / cell cortex / midbody / G alpha (i) signalling events / G alpha (s) signalling events / Extra-nuclear estrogen signaling / cell cycle / cell division / lysosomal membrane / protein domain specific binding / nucleotide binding / GTPase activity / centrosome / GTP binding / nucleolus / Golgi apparatus / protein-containing complex / extracellular exosome / nucleoplasm / membrane / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Tetratricopeptide repeat / Tetratricopeptide repeat ...GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Tetratricopeptide repeat / Tetratricopeptide repeat / G-protein alpha subunit, group I / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / Tetratricopeptide-like helical domain superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(i) subunit alpha-3 / G-protein-signaling modulator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsJia, M. / Li, J. / Zhu, J. / Wen, W. / Zhang, M. / Wang, W.
CitationJournal: To be Published
Title: Crystal Structures of the scaffolding protein LGN reveal the general mechanism by which GoLoco binding motifs inhibit the release of GDP from Galphai subunits in G-coupled heterotrimeric proteins
Authors: Jia, M. / Li, J. / Zhu, J. / Wen, W. / Zhang, M. / Wang, W.
History
DepositionJul 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(k) subunit alpha
B: Guanine nucleotide-binding protein G(k) subunit alpha
C: Guanine nucleotide-binding protein G(k) subunit alpha
D: Guanine nucleotide-binding protein G(k) subunit alpha
E: G-protein-signaling modulator 2
F: G-protein-signaling modulator 2
G: G-protein-signaling modulator 2
H: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,58533
Polymers164,4118
Non-polymers4,17425
Water21612
1
A: Guanine nucleotide-binding protein G(k) subunit alpha
E: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3149
Polymers41,1032
Non-polymers1,2127
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-68 kcal/mol
Surface area16170 Å2
MethodPISA
2
B: Guanine nucleotide-binding protein G(k) subunit alpha
F: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9307
Polymers41,1032
Non-polymers8275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-62 kcal/mol
Surface area15570 Å2
MethodPISA
3
C: Guanine nucleotide-binding protein G(k) subunit alpha
G: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1228
Polymers41,1032
Non-polymers1,0206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-62 kcal/mol
Surface area16560 Å2
MethodPISA
4
D: Guanine nucleotide-binding protein G(k) subunit alpha
H: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2189
Polymers41,1032
Non-polymers1,1167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-69 kcal/mol
Surface area16470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.326, 207.326, 236.545
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#1: Protein
Guanine nucleotide-binding protein G(k) subunit alpha / G(i) alpha-3


Mass: 37888.055 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 25-354 / Mutation: Q147L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI3 / Production host: Escherichia coli (E. coli) / References: UniProt: P08754
#2: Protein/peptide
G-protein-signaling modulator 2 / LGN / Pins homolog


Mass: 3214.632 Da / Num. of mol.: 4 / Fragment: GoLoco 4 (UNP RESIDUES 628-653) / Source method: obtained synthetically / Details: This sequence occurs naturally in mouse. / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8VDU0

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Non-polymers , 4 types, 37 molecules

#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.46 Å3/Da / Density % sol: 72.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.5M ammonium sulfate, 1.0M lithium sulfate monohydrate, 0.1M sodium citrate tribasic dihydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 66825 / Num. obs: 66648 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3280 / % possible all: 11

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 12.494 / SU ML: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.476 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 3375 5.1 %RANDOM
Rwork0.2079 ---
all0.2097 66825 --
obs0.2097 66648 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 160.75 Å2 / Biso mean: 67.426 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10916 0 249 12 11177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211329
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.97515315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.42951358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82624.224535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.544152011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7041571
X-RAY DIFFRACTIONr_chiral_restr0.150.21729
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028363
LS refinement shellResolution: 2.899→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 218 -
Rwork0.327 4244 -
all-4462 -
obs--99.75 %

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